XmlmmCIF equivalent: refine Data items in the REFINE category record details about the structure refinement parameters. XmlmmCIF equivalent: refine/B_iso_max The maximum value for isotropic B value (temperature factors) found in the coordinate set. XmlmmCIF equivalent: refine/B_iso_mean The mean value for isotropic B value (temperature factors) found in the coordinate set. XmlmmCIF equivalent: refine/B_iso_min The minimum value for isotropic B value (temperature factors) found in the coordinate set. XmlmmCIF equivalent: refine/aniso_B11 The [1][1] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/aniso_B12 The [1][2] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/aniso_B13 The [1][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/aniso_B22 The [2][2] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/aniso_B23 The [2][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/aniso_B33 The [3][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. XmlmmCIF equivalent: refine/correlation_coeff_Fo_to_Fc The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - [Fo][Fc]) R~corr~ = ---------------------------------------------------------------------------------------------------------- SQRT{sum~i~(Fo~i~)^2^-[Fo]^2^} SQRT{sum~i~(Fc~i~)^2^-[Fc]^2^} Fo = observed structure factors Fc = calculated structure factors [] = denotes average value summation is over reflections included in the refinement XmlmmCIF equivalent: refine/correlation_coeff_Fo_to_Fc_free The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - [Fo][Fc]) R~corr~ = ----------------------------------------------------------------------------------------------------- SQRT{sum~i~(Fo~i~)^2^-[Fo]^2^} SQRT{sum~i~(Fc~i~)^2^-[Fc]^2^} Fo = observed structure factors Fc = calculated structure factors [] = denotes average value summation is over reflections not included (free reflections) in the refinement XmlmmCIF equivalent: refine/details Description of special aspects of the refinement process. XmlmmCIF equivalent: refine/diff_density_max The maximum value of the electron density in the final difference Fourier map. XmlmmCIF equivalent: refine/diff_density_max_esd The estimated standard deviation of _refine.diff_density_max. XmlmmCIF equivalent: refine/diff_density_min The minimum value of the electron density in the final difference Fourier map. XmlmmCIF equivalent: refine/diff_density_min_esd The estimated standard deviation of _refine.diff_density_min. XmlmmCIF equivalent: refine/diff_density_rms The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density, and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. XmlmmCIF equivalent: refine/diff_density_rms_esd The estimated standard deviation of _refine.diff_density_rms. XmlmmCIF equivalent: refine/ls_R_Fsqd_factor_obs Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the squares of the observed and calculated structure factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure factor amplitudes F~calc~^2^ = squares of the calculated structure factor amplitudes sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_R_I_factor_obs Residual factor R(I) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements of powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------------------------- sum|I~obs~| I~obs~ =the net observed intensities I~calc~ =the net calculated intensities sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_R_factor_R_free Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_R_factor_R_free_error The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. XmlmmCIF equivalent: refine/ls_R_factor_R_free_error_details Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free. XmlmmCIF equivalent: refine/ls_R_factor_R_work Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = -------------------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_R_factor_all Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = ------------------------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_R_factor_obs Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = ------------------------------------ sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_abs_structure_Flack The measure of absolute structure (enantiomorph or polarity) as defined by Flack. The value must be between 0. and 1. with a standard uncertainty (e.s.d.). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. XmlmmCIF equivalent: refine/ls_abs_structure_Flack_esd The estimated standard deviation of _refine.ls_abs_structure_Flack. XmlmmCIF equivalent: refine/ls_abs_structure_Rogers The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. XmlmmCIF equivalent: refine/ls_abs_structure_Rogers_esd The estimated standard deviation of _refine.ls_abs_structure_Rogers. XmlmmCIF equivalent: refine/ls_abs_structure_details The nature of the absolute structure and how it was determined. For example, it may describe the Friedel pairs used. XmlmmCIF equivalent: refine/ls_d_res_high The highest resolution in angstroms for the interplanar spacing in the reflection data used in refinement. This is the smallest d value. XmlmmCIF equivalent: refine/ls_d_res_low The lowest resolution in ansgtroms for the interplanar spacing in the reflection data used in refinement. This is the largest d value. XmlmmCIF equivalent: refine/ls_extinction_coef The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine_ls_extinction_expression and _refine_ls_extinction_method. For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. and Coppens, P. (1974). Acta Cryst. A30,129-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. XmlmmCIF equivalent: refine/ls_extinction_coef_esd The estimated standard deviation of _refine.ls_extinction_coef. XmlmmCIF equivalent: refine/ls_extinction_expression A description or reference of the extinction correction equation used to apply the data item _refine.ls_extinction_coef. This information must be sufficient to reproduce the extinction correction factors applied to the structure factors. XmlmmCIF equivalent: refine/ls_extinction_method A description of the extinction correction method applied with the data item _refine.ls_extinction_coef. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen' The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian'; and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine.details. Ref: Becker, P. J. and Coppens, P. (1974). Acta Cryst. A30, 129-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. XmlmmCIF equivalent: refine/ls_goodness_of_fit_all The least-squares goodness-of-fit parameter S for all data, after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also the definition of _refine.ls_restrained_S_all. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ------------------------------------------------------------------------ ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_goodness_of_fit_all_esd The estimated standard deviation of _refine.ls_goodness_of_fit_all. XmlmmCIF equivalent: refine/ls_goodness_of_fit_obs The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see _reflns.observed_criterion), after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also the definition of _refine.ls_restrained_S_obs. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( --------------------------------------------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_goodness_of_fit_obs_esd The estimated standard deviation of _refine.ls_goodness_of_fit_obs. XmlmmCIF equivalent: refine/ls_hydrogen_treatment Treatment of hydrogen atoms in the least-squares refinement. XmlmmCIF equivalent: refine/ls_matrix_type Type of matrix used to accumulate the least-squares derivatives. XmlmmCIF equivalent: refine/ls_number_constraints The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site_refinement_flags. A general description of constraints may appear in _refine.details. XmlmmCIF equivalent: refine/ls_number_parameters The number of parameters refined in the least-squares process. If possible this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. XmlmmCIF equivalent: refine/ls_number_reflns_R_free The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test (i.e. excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. XmlmmCIF equivalent: refine/ls_number_reflns_R_work The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working (i.e. included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. XmlmmCIF equivalent: refine/ls_number_reflns_all The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. XmlmmCIF equivalent: refine/ls_number_reflns_obs The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. XmlmmCIF equivalent: refine/ls_number_restraints The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Often restrained parameters involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site_refinement_flags. A general description of refinement constraints may appear in _refine.details. XmlmmCIF equivalent: refine/ls_percent_reflns_R_free The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test (i.e. excluded from refinement) reflections when refinement included calculation of a "free" R factor, espressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. XmlmmCIF equivalent: refine/ls_percent_reflns_obs The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. XmlmmCIF equivalent: refine/ls_redundancy_reflns_all The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy those same limits. XmlmmCIF equivalent: refine/ls_redundancy_reflns_obs The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy those same limits. XmlmmCIF equivalent: refine/ls_restrained_S_all The least-squares goodness-of-fit parameter S' for all reflection data, after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_all. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( -------------------------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the observed coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~refr~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflection data sum is taken over the restraint data XmlmmCIF equivalent: refine/ls_restrained_S_obs The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see _reflns.observed_criterion) after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_obs. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ---------------------------------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the observed coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~refr~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflection data sumr is taken over the restraint data XmlmmCIF equivalent: refine/ls_shift_over_esd_max The largest ratio of the final least-squares parameter shift divided by the final standard uncertainty (e.s.d.). XmlmmCIF equivalent: refine/ls_shift_over_esd_mean The average ratio of the final least-squares parameter shift divided by the final standard uncertainty (e.s.d.). XmlmmCIF equivalent: refine/ls_structure_factor_coef Structure-factor coefficient |F|, F^2^ or I, used in the least- squares refinement process. XmlmmCIF equivalent: refine/ls_wR_factor_R_free Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( --------------------------------------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least squares weight sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_wR_factor_R_work Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------------------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least squares weight sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_wR_factor_all Weighted residual factor wR for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( -------------------------------------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least squares weight sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_wR_factor_obs Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the obervation limit established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( -------------------------------------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least squares weight sum is taken over the specified reflections XmlmmCIF equivalent: refine/ls_weighting_details A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of _refine.ls_weighting_scheme is specified as 'calc'. XmlmmCIF equivalent: refine/ls_weighting_scheme The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine_ls_weighting_details for a preferred approach). XmlmmCIF equivalent: refine/occupancy_max The maximum value for occupancy found in the coordinate set. XmlmmCIF equivalent: refine/occupancy_min The minimum value for occupancy found in the coordinate set. XmlmmCIF equivalent: refine/overall_FOM_free_R_set Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. and Dodson, E. J. (1997). Acta Cryst. D53, 240-255. XmlmmCIF equivalent: refine/overall_FOM_work_R_set Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. and Dodson, E. J. (1997). Acta Cryst. D53, 240-255. XmlmmCIF equivalent: refine/overall_SU_B The overall standard uncertainty (e.s.d.) of the thermal parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~B~)^2 gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma~B~)^2 = 8 --------------------------------------------------------- sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation)"Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. and Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation)"Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. and Dodson E. J. (1997). CCP4 Newsletter,no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ XmlmmCIF equivalent: refine/overall_SU_ML The overall standard uncertainty (e.s.d.) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)^2 = ------------------------------------------------------------------ 8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = < cos 2 pi s delta_x > SQRT(Sigma_P/Sigma_N) estimated using maximum likelihoo Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. and Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. and Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ XmlmmCIF equivalent: refine/overall_SU_R_Cruickshank_DPI The overall standard uncertainty (e.s.d.) of the thermal parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ----------------(R_value)^2 (D_min)^2 C^(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R-value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography" Murshudov G. N. and Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ XmlmmCIF equivalent: refine/overall_SU_R_free The overall standard uncertainty (e.s.d.) of the thermal parameters based on the free R value. The overall standard uncertainty gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ---------- (R_free)^2 (D_min)^2 C^(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_free = conventional free crystallographic R-value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. and Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ XmlmmCIF equivalent: refine/pdbx_R_Free_selection_details Details of the manner in which the cross validation reflections were selected. XmlmmCIF equivalent: refine/pdbx_data_cutoff_high_absF Value of F at "high end" of data cutoff. XmlmmCIF equivalent: refine/pdbx_data_cutoff_high_rms_absF Value of RMS |F| used as high data cutoff. XmlmmCIF equivalent: refine/pdbx_data_cutoff_low_absF Value of F at "low end" of data cutoff. XmlmmCIF equivalent: refine/pdbx_isotropic_thermal_model Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. XmlmmCIF equivalent: refine/pdbx_ls_cross_valid_method Whether the cross validataion method was used through out or only at the end. XmlmmCIF equivalent: refine/pdbx_ls_sigma_F Data cutoff (SIGMA(F)) XmlmmCIF equivalent: refine/pdbx_ls_sigma_I Data cutoff (SIGMA(I)) XmlmmCIF equivalent: refine/pdbx_method_to_determine_struct Method(s) used to determine the structure. XmlmmCIF equivalent: refine/pdbx_overall_ESU_R Overall estimated standard uncertainties of positional parameters based on R value. XmlmmCIF equivalent: refine/pdbx_overall_ESU_R_Free Overall estimated standard uncertainties of positional parameters based on R value. XmlmmCIF equivalent: refine/pdbx_solvent_ion_probe_radii CCP4 solvent ion proble radii XmlmmCIF equivalent: refine/pdbx_solvent_shrinkage_radii CCP4 solvent shrinkage radii XmlmmCIF equivalent: refine/pdbx_solvent_vdw_probe_radii CCP4 solvent proble van der Waals radii XmlmmCIF equivalent: refine/pdbx_starting_model Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. XmlmmCIF equivalent: refine/pdbx_stereochem_target_val_spec_case Special case of stereochemistry target values used in SHELXL refinement. XmlmmCIF equivalent: refine/pdbx_stereochemistry_target_values Stereochemistry target values used in refinement. XmlmmCIF equivalent: refine/solvent_model_details Special aspects of the solvent model used in refinement. XmlmmCIF equivalent: refine/solvent_model_param_bsol The value of the BSOL solvent model parameter describing the average isotropic temperature factor of disordered solvent atoms. XmlmmCIF equivalent: refine/solvent_model_param_ksol The value of the KSOL solvent model parameter describing the ratio of electron density in the bulk solvent to the electron density in the molecular solute. XmlmmCIF equivalent: refine/entry_id This data item is a pointer to _entry.id in the ENTRY category.